The prion hypothesis provides an explanation for a diverse collection of previously inexplicable phenomena, ranging from the appearance, progression and spread of neurodegenerative disease in mammals to the non- Mendelian inheritance of unique traits in fungi. According to this idea, prion-associated phenotypes arise when a prion protein adopts an alternative physical state and persist when that form self-replicates. This self- replication is mediated by the assembly of alternatively folded prion protein into aggregates, which template the conversion of other forms of the protein to a like state. The inherent ability of prion proteins to harness their conformational flexibility is a central event in establishing distinct phenotypes, but the extension of this process to practice becomes a multistep endeavor within the context of a living cell. Protein quality control pathways, prion protein biogenesis, and cell biology all modify prion protein misfolding in vivo to create transmissible changes in physiology. A molecular understanding of how these forces intersect is a clear gap in current knowledge, limiting our ability to correlate protein misfolding mechanisms in vitro and disease mechanisms in vivo. As the appearance, spread and reversal of prion-associated phenotypes necessarily involve changes in protein state, these forces must converge on events that regulate transitions between prion forms. The long-term goal of this research is to elucidate the molecular mechanisms allowing prion proteins to act as elements of disease and heritability by developing an understanding of the interplay between prion protein dynamics and its cellular context. The overall objective of this application is to determine how the physical characteristics of prion proteins modulate prion aggregate dynamics to create distinct phenotypes. The central hypothesis is that specific sequence elements within prion proteins impact their recognition and/or processing by molecular chaperones, creating a continuum of dynamic systems that allow distinct phenotypes to appear and persist but also to occasionally interconvert. Guided by strong preliminary data using the experimentally tractable Sup35/[PSI+] prion of S. cerevisiae, this hypothesis will be tested through three specific aims: 1) Deter- mine the molecular mechanism by which sequence variants of Sup35 alter prion propagation, 2) Determine the molecular mechanism by which excess Hsp104 leads to prion loss, and 3) Determine the molecular basis of the Sup35/[PSI+] prion phenotype. These proposed studies are innovative because they use a unique combination of experimental and mathematical analyses to temporally link transitions in prion protein physical and functional state. The proposed research is significant because it will provide a new and dynamic framework for exploring the relationship between prion protein misfolding and its physiological consequences. Given the remarkable similarity of prion sequences and misfolding pathways from yeast to man, these observations will be broadly applicable to the wide range of biological events regulated by these fascinating proteins.